gov.usda.gdpc
Class Chromosome

java.lang.Object
  gov.usda.gdpc.AbstractGroup
      gov.usda.gdpc.AbstractDBElementGroup
          gov.usda.gdpc.AbstractLocusGroup
              gov.usda.gdpc.Chromosome

All Implemented Interfaces:

java.util.Collection, DBElementGroup, Group, java.util.List, LocusGroup

public final class Chromosome

extends AbstractLocusGroup

Author:

terryc

Field Summary

Fields inherited from class gov.usda.gdpc.AbstractDBElementGroup

myIndex

Constructor Summary

Chromosome(int number)
Chromosome constructor.

Chromosome(int number, java.util.List list)
Chromosome constructor.

Chromosome(int number, Locus[] loci)
Chromosome Constructor

Chromosome(int number, LocusGroup[] groups)
Chromosome constructor.

Method Summary

Locus	getCentromereLocation() Get centromere location.
double	getGeneticCenterPosition() Get numeric genetic center position of chromosome.
double	getGeneticPositionRange() Get genetic positions range shown on big image.
double	getMaxGeneticPosition() Get the maximum genetic position.
double	getMinGeneticPosition() Get the minimum genetic position.
java.lang.String	getType() Get type of this group.
java.lang.String	toString() String representation of this chromosome

Methods inherited from class gov.usda.gdpc.AbstractLocusGroup

getLocus, getLocusGroup

Methods inherited from class gov.usda.gdpc.AbstractDBElementGroup

getDBElementGroup, getDBElements, getDefinedProperties, getDistinctProperties, index

Methods inherited from class gov.usda.gdpc.AbstractGroup

add, add, addAll, addAll, clear, contains, containsAll, get, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, retainAll, set, size, subList, toArray, toArray

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface gov.usda.gdpc.DBElementGroup

getDBElements, getDefinedProperties, getDistinctProperties, index

Methods inherited from interface java.util.List

add, add, addAll, addAll, clear, contains, containsAll, equals, get, hashCode, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, retainAll, set, size, subList, toArray, toArray

Constructor Detail

Chromosome

public Chromosome(int number,
                  Locus[] loci)

Chromosome Constructor

Parameters:

number - chromosome number

loci - list of loci

Chromosome

public Chromosome(int number)

Chromosome constructor. Creates an empty group.

Parameters:

number - chromosome number

Chromosome

public Chromosome(int number,
                  java.util.List list)

Chromosome constructor.

Parameters:

number - chromosome number

list - list of objects to be a part of this group. Any null in the list will be discarded.

Chromosome

public Chromosome(int number,
                  LocusGroup[] groups)

Chromosome constructor.

Parameters:

number - chromosome number

groups - groups to include in this new group.

Method Detail

getMinGeneticPosition

public double getMinGeneticPosition()

Get the minimum genetic position.

Returns:

minimum genetic position

getMaxGeneticPosition

public double getMaxGeneticPosition()

Get the maximum genetic position.

Returns:

maximum genetic position

getCentromereLocation

public Locus getCentromereLocation()

Get centromere location.

Returns:

centromere location

getGeneticPositionRange

public double getGeneticPositionRange()

Get genetic positions range shown on big image.

Returns:

genetic position range

getGeneticCenterPosition

public double getGeneticCenterPosition()

Get numeric genetic center position of chromosome.

Returns:

genetic center position

toString

public java.lang.String toString()

String representation of this chromosome

Overrides:

toString in class AbstractDBElementGroup

Returns:

string representation

getType

public java.lang.String getType()

Get type of this group.

Specified by:

getType in interface DBElementGroup

Overrides:

getType in class AbstractLocusGroup

Returns:

type